## `summarise()` has grouped output by 'patient', 'age_at_sample_exact', 'age_at_sample', 'DOB', 'DATE_OF_DIAGNOSIS'. You can override using the `.groups` argument.
## Joining, by = "PDID"
| patient | ID | age_at_sample_exact | cell_type | phase | BaitLabel |
|---|---|---|---|---|---|
| PD5847 | COLONY45 | 44.89802 | BFU-E-Colony | Colony | NA |
| PD5847 | PD5847i | 44.91170 | BM Gran | Recapture | PD5847i |
| PD5847 | PD5847j | 45.64271 | PB Gran | Recapture | PD5847j |
| PD5847 | PD5847k | 45.91102 | PB Gran | Recapture | PD5847k |
| PD5847 | PD5847l | 49.11157 | PB Gran | Recapture | PD5847l |
tree=plot_basic_tree(PD$pdx,label = PD$patient,style="classic")
The nodes in this plot can be cross-referenced with nodes specified in subsequent results. The plot also serves to give an idea of what the topology at the top of the tree looks like.
tree=plot_basic_tree(expand_short_branches(PD$pdx,prop = 0.1),label = PD$patient,style="classic")
node_labels(tree)
Note that the different colours on the tree indicate the separately fitted mutation rate clades.
##
## Random-Effects Model (k = 1; tau^2 estimator: REML)
##
## logLik deviance AIC BIC AICc
## -0.0000 0.0000 4.0000 -Inf 16.0000
##
## tau^2 (estimated amount of total heterogeneity): 0
## tau (square root of estimated tau^2 value): 0
## I^2 (total heterogeneity / total variability): 0.00%
## H^2 (total variability / sampling variability): 1.00
##
## Test for Heterogeneity:
## Q(df = 0) = 0.0000, p-val = 1.0000
##
## Model Results:
##
## estimate se zval pval ci.lb ci.ub
## 17.9355 0.4921 36.4484 <.0001 16.9711 18.9000 ***
##
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
| node | driver | status | child_count | type | colony_count | mean_lambda_rescaled | correction | sd_rescaled | lb_rescaled | ub_rescaled | median_rescaled | p_lt_wt |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| -1 | WT | 1 | -1 | local | 15 | 17.93552 | 1.01721 | 0.2421426 | 17.46584 | 18.42420 | 17.93146 | NA |
| 100 | JAK2,9pUPD | 1 | 77 | local | 6 | 21.14323 | 1.01721 | 1.2996510 | 19.18960 | 24.25722 | 20.92220 | 3.5e-04 |
| 187 | DNMT3A | 1 | 4 | local | 4 | 20.10593 | 1.01721 | 0.5447833 | 19.07923 | 21.20959 | 20.09224 | 5.0e-05 |
| 104 | TET2:JAK2,9pUPD | 1 | 71 | local | 71 | 23.06632 | 1.01721 | 1.6688739 | 20.27521 | 26.82576 | 22.90158 | 2.5e-05 |
All ages are in terms of post conception years. The vertical red lines denote when colonies were sampled and blue lines when targeted follow up samples were taken.
| patient | node | driver | child_count | lower_median | upper_median | lower_lb95 | lower_ub95 | upper_lb95 | upper_ub95 | N | group | age_at_diagnosis_pcy | max_age_at_sample | min_age_at_sample |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PD5847 | 187 | DNMT3A | 4 | 0.0325864 | 0.1635204 | 0.0177970 | 0.0664861 | 0.1035941 | 0.3409181 | 5 | DNMT3A | 45.62355 | 49.83984 | 45.62628 |
| PD5847 | 100 | JAK2,9pUPD | 77 | 0.0075348 | 26.3679458 | 0.0046611 | 0.0252664 | 24.6548616 | 28.9069826 | 5 | JAK2 | 45.62355 | 49.83984 | 45.62628 |
| PD5847 | 104 | TET2 | 71 | 27.1489740 | 33.6900388 | 25.4655497 | 29.5969825 | 32.1823043 | 35.4263396 | 5 | TET2 | 45.62355 | 49.83984 | 45.62628 |
## Timings using the Clade Specific Rates
| label | node | het.sensitivity | chr | start | end | nhet | nhom | mean_loh_event | lower_loh_event | upper_loh_event | t_before_end | t_before_end_lower | t_before_end_upper | kb | count_in_bin | count_se | pmut | pmut_se | xmean | xse_mean | xsd | x2.5. | x50. | x97.5. | xn_eff | xRhat | lmean | lse_mean | patient | driver3 | child_count |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 9pUPD | 100 | 0.9917 | 9 | 10469 | 47206190 | 0 | 10 | 24.75 | 20.4 | 26.44 | 1.743 | 0.04495 | 6.092 | 47200000 | 7744 | 88 | 0.01691 | 0.0001922 | 0.9342 | 0.0003936 | 0.06168 | 0.7699 | 0.9518 | 0.9983 | 24557 | 1 | 7.402 | 0.0006372 | PD5847 | JAK2,9pUPD | 77 |
Here we exclude all local CNAs and depict as color VAF plots